Hi Troels, Thanks for the quick response!
Protein 1: I will attempt to troubleshoot using the advice you gave me. The problem occurs write after it indicates its writing a file for prolate round_3 (so its about to start it). I will run it again and post the output to give you a better idea. I'm pretty sure the output was something like this Over-fit spin deselection: No spins have been deselected. Resetting the minimisation statistics. But I will double check and send you another email with the actual output. Protein 2: I am using the sample script for dAuvergene protocol. So the only thing I've changed since my previous run (the one that worked that you wrote a tutorial for), was the pdb file and the data set I used. The thing I suspected was causing an issue ,was the pdb file since I slightly modified it, and thats really the only thing different from this run versus the others. Also side note, if I were to deselect the spins that I don't have data for or I have bad data for, that wouldn't change any of the calculations correct? I never have since I assumed relax would just ignore all the amino acids I don't have data for, but it may help increase the speed of my calculations if I just tell relax to just ignore the spins from the start. Sincerely, Sam On Mon, Sep 19, 2016 at 9:12 AM, Troels Emtekær Linnet < tlin...@nmr-relax.com> wrote: > Hi Sam. > > Happy to hear you that you get some progress. > > Protein 1: > Can you help me to find out, if you are minimizing or running Monte-Carlo > simulations? > This COULD be the problem: > > How relax works (at least how it works for relaxation dispersion): > Step 1: Minimize the error for the target function. Find the parameters > which best match the target function to the data, by minimizing the error. > Here each individual spin minimization is handed out to a processor for > calculation. > > Step 2: Determine the error of the minimization by monte carlo simulations. > Create (Standard 500) additional datasets with a copy from the original. > Modify each datapoint by an error, drawn from a gaussian distribution where > the width is described by the error of measurements. > Now hand out each of the datasets to the processor. Each processor should > now calculate the minimization for all the spins. The minimization should > be more quick, as the starting position is chosen from Step 1. > > Possible problem: One (or more) of the spins has really bad data. So a > little change of the data makes the minimization space very different. > Think of a flat table. Where should the "minimization ball" run into? > Maybe you have created a small new bump in the table. This is typically for > "bad" data. > > This could either be the measurement OR the error estimation. Relax will > keep on searching for minimization. > If you are "unlucky", some of the created datasets will make relax hang > for a very long time. > > Unfortunately, it is NOT possible to ask a processor about its "current" > work, when it is doing a minimization for a whole dataset. > And if it was, it would create an output of 64 spins being minimized at > the same time, creating a big mess, since the processors are working alone. > When doing Monte-Carlo simulations, relax are quite silent. Only reporting > when a whole dataset is done. > > Is relax stuck in Monte-Carlo simulations? > > Possible solution: > *) Set Monte-Carlo simulations to 3 (which is minimum), and know that you > have found the right minimum, but the error estimation of the parameters > are wrong. > *) Carefully inspect your data, deselecting all spins which have "bad > data". Look at their graphs. Consider working with as few spins as > possible, and work your way up! Working this way will greatly increase your > productivity. > > Protein 2: > Are you setting the bonds for the minimization manually? > This looks like the upper/lower bonds are specified wrong. This is not > easy to do. How are you doing it? > > Best > Troels > > > > > 2016-09-19 17:11 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>: > >> Hi Troels, >> >> I have successfully been able to run the model-free analysis on 64 cores. >> The issue appears to have been I simply did not specify the spin number, so >> after looking at your tutorial and making the proper modifications, it ran >> with no complications. The results are somewhat reasonable. I decided to >> try to run 2 other proteins however; and I've come across problems for both >> again. >> Protein 1: >> I set this up just like the tutorial, and it runs with no warnings or >> errors; however, the run never finishes. At round_3 for the prolate model >> when it starts to minimize it just stops. I don't mean relax is stopped or >> closed, I mean it stops doing any calculations. Relax is still open, and if >> I run the top command, I can still see something is going on with the other >> cores, but nothing is being calculated. The run with 64 cores is incredibly >> fast (under 4 hours), so I don't think it's loading calculations or writing >> them, and I've left it there for over 24 hours, and it's still just sorta >> stuck. There are no errors, no outputs, it just says its gonna start to >> minimize and then nothing happens after that. >> Protein2: >> This protein was a little different since the pdb structure was a crystal >> structure. I had to use WhatIf to add the protons onto the pdb file. The >> structure appears to load up fine, all the spins appear to be read, data is >> loaded, vectors and are calculated and define, but when I came to run the >> protocol this error pops up: >> File "/home/sam2/relax-4.0.2/multi/processor.py", line 494, in run >> self.callback.init_master(self) >> File "/home/sam2/relax-4.0.2/multi/__init__.py", line 318, in >> default_init_master >> self.master.run() >> File "/home/sam2/relax-4.0.2/relax.py", line 199, in run >> self.interpreter.run(self.script_file) >> File "/home/sam2/relax-4.0.2/prompt/interpreter.py", line 279, in run >> return run_script(intro=self.__intro_string, local=locals(), >> script_file=script_file, show_script=self.__show_script, >> raise_relax_error=self.__raise_relax_error) >> File "/home/sam2/relax-4.0.2/prompt/interpreter.py", line 585, in >> run_script >> return console.interact(intro, local, script_file, >> show_script=show_script, raise_relax_error=raise_relax_error) >> File "/home/sam2/relax-4.0.2/prompt/interpreter.py", line 484, in >> interact_script >> exec_script(script_file, local) >> File "/home/sam2/relax-4.0.2/prompt/interpreter.py", line 363, in >> exec_script >> runpy.run_module(module, globals) >> File "/usr/lib64/python2.7/runpy.py", line 192, in run_module >> fname, loader, pkg_name) >> File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code >> exec code in run_globals >> File "/home/sam2/relax-4.0.2/HdeA_script.py", line 30, in <module> >> dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,di >> ff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=LOCA >> L_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_ALGOR,mc_sim_ >> num=MC_NUM,conv_loop=CONV_LOOP) >> File "/home/sam2/relax-4.0.2/auto_analyses/dauvergne_protocol.py", >> line 246, in __init__ >> self.execute() >> File "/home/sam2/relax-4.0.2/auto_analyses/dauvergne_protocol.py", >> line 600, in execute >> self.multi_model(local_tm=True) >> File "/home/sam2/relax-4.0.2/auto_analyses/dauvergne_protocol.py", >> line 888, in multi_model >> self.interpreter.minimise.grid_search(inc=self.grid_inc) >> File "/home/sam2/relax-4.0.2/prompt/uf_objects.py", line 225, in >> __call__ >> self._backend(*new_args, **uf_kargs) >> File "/home/sam2/relax-4.0.2/pipe_control/minimise.py", line 172, in >> grid_search >> model_lower, model_upper, model_inc = grid_setup(lower, upper, inc, >> verbosity=verbosity, skip_preset=skip_preset) >> File "/home/sam2/relax-4.0.2/pipe_control/minimise.py", line 341, in >> grid_setup >> elif values[i] in [None, {}, []]: >> IndexError: index 0 is out of bounds for axis 0 with size 0 >> I should mention this error pops up when it decided to calculate the >> first spins upper and lower bounds. So this isn't at the minimization >> portion of the calculation (like in the previous bug). Thanks in advance. >> >> Sincerely, >> Sam >> >> On Wed, Sep 14, 2016 at 6:34 AM, Troels Emtekær Linnet < >> tlin...@nmr-relax.com> wrote: >> >>> Hi Sam. >>> >>> To tackle this problem, I would advice to create another bug. >>> Creation and closing of a bug "leaves trails", which maybe will help >>> another person, when googling for the same problem. >>> >>> To help you, can you do a "relax -i" on both computers? >>> That give some indication about package versions and computer setup. >>> >>> The first thing we need to establish, is that mpirun is working. >>> We have to test the installation without relax. >>> >>> Can you have a look at: >>> http://wiki.nmr-relax.com/OpenMPI >>> >>> Try the different things like: >>> lscpu >>> mpirun --report-bindings -np 11 echo "hello world" >>> mpirun --report-bindings -np 4 relax --multi='mpi4py' >>> >>> When we are confident about this, then we will try make a small test >>> script for relax. >>> >>> Please try these things at both computers, and provide 2 files with >>> commands and output. >>> >>> Then attach it to the bug report. >>> >>> >>> >>> >>> >>> 2016-09-14 6:40 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>: >>> >>>> Hi Troels, >>>> >>>> So I saw the tutorial you put, and the main problem was I had not >>>> specified my data was only for the Nitrogen spins. After applying the spin >>>> column, my data loaded and relax ran model free with no problem. I have a >>>> script that starts and runs relax and model free all automatic, if you wish >>>> I can send it via email to you and you can upload it to the tutorial wiki >>>> page. So I can successfully run model-free in script mode for a >>>> uni-processor. >>>> The problem now with the multi-processor is that the script won't load. >>>> In the bug page I uploaded a screenshot where I had input the 'mpirun -np 4 >>>> ../relax --multi='mpi4py' command, however I had no output. I checked >>>> processes running in the background, and saw that there was indeed 4 >>>> processess running in the background (1 master and 3 slaves) for relax; but >>>> there was no output, so I was unable to load any data, or create a pipe or >>>> anything. This was only on the Fedora 24 computer, not the Fedora 20. On >>>> the Fedora 20 computer, I was able to successfully open relax on a multi >>>> processor platform. I can send the screenshots and the relax -i for both >>>> computers again. I don't know why it doesn't work the fedora 24. Do you >>>> know what could be causing this? >>>> >>>> Thanks again in advance >>>> >>>> On Tue, Sep 13, 2016 at 9:32 PM, Troels Emtekær Linnet < >>>> tlin...@nmr-relax.com> wrote: >>>> >>>>> Hi Sam >>>>> >>>>> Can you send the mail again and include the maillist? >>>>> >>>>> Best Troels >>>>> >>>>> >>>>> Den tirsdag den 13. september 2016 skrev Mahdi, Sam < >>>>> sam.mahdi....@my.csun.edu>: >>>>> >>>>>> HI Troels, >>>>>> >>>>>> So I saw the tutorial you put, and the main problem was I had not >>>>>> specified my data was only for the Nitrogen spins. After applying the >>>>>> spin >>>>>> column, my data loaded and relax ran model free with no problem. I have a >>>>>> script that starts and runs relax and model free all automatic, if you >>>>>> wish >>>>>> I can send it via email to you and you can upload it to the tutorial wiki >>>>>> page. So I can successfully run model-free in script mode for a >>>>>> uni-processor. >>>>>> The problem now with the multi-processor is that the script won't >>>>>> load. In the bug page I uploaded a screenshot where I had input the >>>>>> 'mpirun >>>>>> -np 4 ../relax --multi='mpi4py' command, however I had no output. I >>>>>> checked >>>>>> processes running in the background, and saw that there was indeed 4 >>>>>> processess running in the background (1 master and 3 slaves) for relax; >>>>>> but >>>>>> there was no output, so I was unable to load any data, or create a pipe >>>>>> or >>>>>> anything. This was only on the Fedora 24 computer, not the Fedora 20. On >>>>>> the Fedora 20 computer, I was able to successfully open relax on a multi >>>>>> processor platform. I can send the screenshots and the relax -i for both >>>>>> computers again. I don't know why it doesn't work the fedora 24. Do you >>>>>> know what could be causing this? >>>>>> >>>>>> Thanks again in advance >>>>>> Sam >>>>>> >>>>>> On Tue, Sep 13, 2016 at 1:01 PM, Troels Emtekær Linnet < >>>>>> tlin...@nmr-relax.com> wrote: >>>>>> >>>>>>> Hi Sam. >>>>>>> >>>>>>> I closed the 2 bug reports as invalid. >>>>>>> >>>>>>> The data is not labelled correct. >>>>>>> But this can be corrected. >>>>>>> >>>>>>> Please see this tutorial I wrote: >>>>>>> http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_sam_mahdi >>>>>>> >>>>>>> I hope this give some guidance. >>>>>>> >>>>>>> If you experience any new problems, please feel free to ask!! >>>>>>> >>>>>>> What you experience, will probably be the same for many. >>>>>>> Your feedback is valuable for the development. >>>>>>> >>>>>>> Please wait with using mpirun and multiple processors, before you >>>>>>> are absolutely sure >>>>>>> that it will run on 1 processor. >>>>>>> >>>>>>> Bugfixing when using multiple processors is a nightmare.... >>>>>>> >>>>>>> Best >>>>>>> Troels >>>>>>> >>>>>>> 2016-09-12 17:36 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>: >>>>>>> >>>>>>>> Hi Troels, >>>>>>>> >>>>>>>> I just created another bug report. I simply copy pasted the email, >>>>>>>> and uploaded the script files there. >>>>>>>> >>>>>>>> Sincerely, >>>>>>>> Sam >>>>>>>> >>>>>>>> On Mon, Sep 12, 2016 at 5:14 AM, Troels Emtekær Linnet < >>>>>>>> tlin...@nmr-relax.com> wrote: >>>>>>>> >>>>>>>>> Hi Sam. >>>>>>>>> >>>>>>>>> Can you produce another bug report. >>>>>>>>> >>>>>>>>> Please don't attach files to these mails as it will strain the >>>>>>>>> mailinglists. >>>>>>>>> >>>>>>>>> Cheers >>>>>>>>> Troels >>>>>>>>> >>>>>>>>> >>>>>>>>> Den lørdag den 10. september 2016 skrev Mahdi, Sam < >>>>>>>>> sam.mahdi....@my.csun.edu>: >>>>>>>>> >>>>>>>>>> Hi Troels, >>>>>>>>>> >>>>>>>>>> Additional question that I had, if you could also look into this >>>>>>>>>> as well on Tuesday please. I have decided to try to write a script to >>>>>>>>>> automate this whole process (since I won't be using the gui to do >>>>>>>>>> model >>>>>>>>>> free), and I've come across a problem. I can successfully open up >>>>>>>>>> relax >>>>>>>>>> using openmpi, and can load the pdb file, and assign all the spins >>>>>>>>>> and >>>>>>>>>> isotopes; however, it appears it will only load one data file (the >>>>>>>>>> very >>>>>>>>>> first one I'll have inputed in the script). I don't know if there is >>>>>>>>>> a >>>>>>>>>> problem with how I wrote my script. Not only will it not load the >>>>>>>>>> rest of >>>>>>>>>> my data sets, it won't actually run dAuvergne's protocol either, >>>>>>>>>> it'll just >>>>>>>>>> load the data set and exit out of the program. Attached is the >>>>>>>>>> script I >>>>>>>>>> wrote for relax. >>>>>>>>>> >>>>>>>>>> This is the output once relax has loaded >>>>>>>>>> >>>>>>>>>> script = 'model_free_sample_script.py' >>>>>>>>>> ------------------------------------------------------------ >>>>>>>>>> ---------------------------------------- >>>>>>>>>> from time import asctime, localtime >>>>>>>>>> from auto_analyses.dauvergne_protocol import dAuvergne_protocol >>>>>>>>>> DIFF_MODEL=['local_tm','sphere','prolate','oblate','ellipsoi >>>>>>>>>> d','final'] >>>>>>>>>> MF_MODELS=['m0','m1','m2','m3','m4','m5','m6','m7','m8','m9'] >>>>>>>>>> LOCAL_TM_MODELS=['tm0','tm1','tm2','tm3','tm4','tm5','tm6',' >>>>>>>>>> tm7','tm7','tm8','tm9'] >>>>>>>>>> GRID_INC=11 >>>>>>>>>> MIN_ALGOR='newton' >>>>>>>>>> MC_NUM=500 >>>>>>>>>> CONV_LOOP=True >>>>>>>>>> pipe_bundle="mf(%s)"%asctime(localtime()) >>>>>>>>>> name="origin-"+pipe_bundle >>>>>>>>>> pipe.create(name,'mf',bundle=pipe_bundle) >>>>>>>>>> structure.read_pdb('2d9j.pdb',set_mol_name='hRGS7') >>>>>>>>>> structure.load_spins('@N',ave_pos=True) >>>>>>>>>> structure.load_spins('@NE1',ave_pos=True) >>>>>>>>>> structure.load_spins('@H',ave_pos=True) >>>>>>>>>> structure.load_spins('@HE1',ave_pos=True) >>>>>>>>>> spin.isotope('15N',spin_id='@N*') >>>>>>>>>> spin.isotope('1H',spin_id='@H*') >>>>>>>>>> relax_data.read(ri_id='R1_Agnes',ri_type='R1',frq=599.642*1e6, >>>>>>>>>> file='R1_Agnes',res_num_col=1,data_col=2,error_col=3) >>>>>>>>>> relax_data.read(ri_id='R2_Agnes',ri_type='R2',frq=599.642*1e6, >>>>>>>>>> file='R2_Agnes',res_num_col=1,data_col=2,error_col=3) >>>>>>>>>> relax_data.read(ri_id='ssNOE_Agnes',ri_type='NOE',frq=599.642*1e6, >>>>>>>>>> file='ssNOE_Agnes',res_num_col=1,data_col=2,error_col=3) >>>>>>>>>> relax_data.read(ri_id='R1_NMRFAM',ri_type='R1',frq=799.642*1e6, >>>>>>>>>> file='R1_NMRFAM',res_num_col=1,data_col=2,error_col=3) >>>>>>>>>> relax_data.read(ri_id='R2_NMRFAM',ri_type='R2',frq=799.642*1e6, >>>>>>>>>> file='R2_NMRFAM',res_num_col=1,data_col=2,error_col=3) >>>>>>>>>> relax_data.read(ri_id='ssNOE_NMRFAM',ri_type='NOE',frq=799.642*1e6, >>>>>>>>>> file='ssNOE_NMRFAM',res_num_col=1,data_col=2,error_col=3) >>>>>>>>>> interatom.define(spin_id1='@N',spin_id2='@H', direct_bond=True) >>>>>>>>>> interatom.define(spin_id1='@NE1',spin_id2='@HE1', >>>>>>>>>> direct_bond=True) >>>>>>>>>> interatom.set_dist(spin_id1='@N*',spin_id2='@H*',ave_dist=1. >>>>>>>>>> 02*1e-10) >>>>>>>>>> interatom.unit_vectors() >>>>>>>>>> value.set(-172*1e-6,'csa',spin_id='@N*') >>>>>>>>>> dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,di >>>>>>>>>> ff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=LOCA >>>>>>>>>> L_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_ALGOR,mc_sim_num >>>>>>>>>> =MC_NUM,conv_loop=CONV_LOOP) >>>>>>>>>> >>>>>>>>>> So it indicates that my script has loaded. However, after it >>>>>>>>>> loads the spins from the pdb file, this is what happens after my >>>>>>>>>> first data >>>>>>>>>> set has been loaded: >>>>>>>>>> >>>>>>>>>> relax> relax_data.read(ri_id='R1_Agnes', ri_type='R1', >>>>>>>>>> frq=599642000.0, file='R1_Agnes', dir=None, spin_id_col=None, >>>>>>>>>> mol_name_col=None, res_num_col=1, res_name_col=None, >>>>>>>>>> spin_num_col=None, >>>>>>>>>> spin_name_col=None, data_col=2, error_col=3, sep=None, spin_id=None) >>>>>>>>>> Opening the file 'R1_Agnes' for reading. >>>>>>>>>> RelaxWarning: The sequence data in the line ['Residue', 'R1', >>>>>>>>>> 'Error'] is invalid, the residue number data 'Residue' is invalid. >>>>>>>>>> RelaxWarning: The sequence data in the line ['1'] is invalid, the >>>>>>>>>> data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['2'] is invalid, the >>>>>>>>>> data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['3'] is invalid, the >>>>>>>>>> data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['4'] is invalid, the >>>>>>>>>> data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['5'] is invalid, the >>>>>>>>>> data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['6'] is invalid, the >>>>>>>>>> data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['7'] is invalid, the >>>>>>>>>> data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['8'] is invalid, the >>>>>>>>>> data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['9'] is invalid, the >>>>>>>>>> data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['10'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['11'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['16'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['17'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['18'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['21'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['22'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['23'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['26'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['27'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['28'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['31'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['40'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['46'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['58'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['61'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['62'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['63'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['73'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['76'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['79'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['81'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['82'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['85'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['94'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['97'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['99'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['106'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['115'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['121'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['126'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['127'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['134'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['135'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['136'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['137'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> RelaxWarning: The sequence data in the line ['139'] is invalid, >>>>>>>>>> the data is missing. >>>>>>>>>> >>>>>>>>>> RelaxError: The spin ID '#hRGS7:12' corresponds to multiple >>>>>>>>>> spins, including '#hRGS7:12@N' and '#hRGS7:12@H'. >>>>>>>>>> crowlab: [~/relax-4.0.2]> >>>>>>>>>> >>>>>>>>>> As you can see, I have all 6 data sets set to load, but only the >>>>>>>>>> very first one appears to do so, and after it loads, it just exits >>>>>>>>>> out of >>>>>>>>>> relax. Again, I don't know if this is a problem with how I wrote the >>>>>>>>>> script. The Relax_script1 is the one that I load up to run the whole >>>>>>>>>> thing. >>>>>>>>>> The model free script.py is just the script it reads once relax has >>>>>>>>>> opened >>>>>>>>>> up. Again, I can see all the spins are properly loaded, and the >>>>>>>>>> isotopes >>>>>>>>>> are set. It just everything after the first data set that doesn't >>>>>>>>>> load. >>>>>>>>>> Thanks again in advance. >>>>>>>>>> >>>>>>>>>> Sincerely, >>>>>>>>>> Sam >>>>>>>>>> >>>>>>>>>> On Thu, Sep 8, 2016 at 10:15 AM, Mahdi, Sam < >>>>>>>>>> sam.mahdi....@my.csun.edu> wrote: >>>>>>>>>> >>>>>>>>>>> Hi Troels, >>>>>>>>>>> >>>>>>>>>>> Thank you so much. If there is any extra info you need please >>>>>>>>>>> let me know. >>>>>>>>>>> >>>>>>>>>>> Sincerely, >>>>>>>>>>> Sam >>>>>>>>>>> >>>>>>>>>>> On Thu, Sep 8, 2016 at 9:12 AM, Troels Emtekær Linnet < >>>>>>>>>>> tlin...@nmr-relax.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi Sam. >>>>>>>>>>>> >>>>>>>>>>>> I will have some time on Tuesday, and then I will look at it. >>>>>>>>>>>> >>>>>>>>>>>> Best >>>>>>>>>>>> Troels >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> Den onsdag den 7. september 2016 skrev Mahdi, Sam < >>>>>>>>>>>> sam.mahdi....@my.csun.edu>: >>>>>>>>>>>> >>>>>>>>>>>>> Hello Troels, >>>>>>>>>>>>> >>>>>>>>>>>>> I uploaded all the files, and even added in the entire output >>>>>>>>>>>>> that i recieved using model free in script mode. I didn't know if >>>>>>>>>>>>> all the >>>>>>>>>>>>> files uploaded need to have that link, so only the initial files >>>>>>>>>>>>> that were >>>>>>>>>>>>> uploaded it, have it. >>>>>>>>>>>>> Thank you in advance for your help! >>>>>>>>>>>>> Sincerely, >>>>>>>>>>>>> Sam >>>>>>>>>>>>> >>>>>>>>>>>>> On Wed, Sep 7, 2016 at 12:41 AM, Troels Emtekær Linnet < >>>>>>>>>>>>> tlin...@nmr-relax.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sam. >>>>>>>>>>>>>> >>>>>>>>>>>>>> You should be able to upload more files after the initial >>>>>>>>>>>>>> upload. >>>>>>>>>>>>>> In the comment thread, please also make a link to this >>>>>>>>>>>>>> discussion. >>>>>>>>>>>>>> >>>>>>>>>>>>>> https://mail.gna.org/public/relax-users/2016-09/threads.html >>>>>>>>>>>>>> #00001 >>>>>>>>>>>>>> >>>>>>>>>>>>>> Best >>>>>>>>>>>>>> Troels >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> 2016-09-06 19:10 GMT+02:00 Mahdi, Sam < >>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thank you for your reply. When I come to upload my data >>>>>>>>>>>>>>> though, I see there are only 4 available slots I can upload my >>>>>>>>>>>>>>> data. I have >>>>>>>>>>>>>>> a total of 6 data files however, that need to be uploaded (3 of >>>>>>>>>>>>>>> each >>>>>>>>>>>>>>> frequency). I also need to upload the relax -i of 2 different >>>>>>>>>>>>>>> computers, >>>>>>>>>>>>>>> and the script file I've been using for a total of 9 files that >>>>>>>>>>>>>>> need to be >>>>>>>>>>>>>>> uploaded. Is there a way to increase the amount I can upload, >>>>>>>>>>>>>>> or can I >>>>>>>>>>>>>>> upload more after the initial submission? >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Mon, Sep 5, 2016 at 2:46 AM, Troels Emtekær Linnet < >>>>>>>>>>>>>>> tlin...@nmr-relax.com> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Sam. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> To solve this problem, it would be easier to have access to >>>>>>>>>>>>>>>> some of your data. >>>>>>>>>>>>>>>> Can you upload to: https://gna.org/bugs/?group=relax >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Take each of your data files, and delete all data, except 2 >>>>>>>>>>>>>>>> spins. >>>>>>>>>>>>>>>> Also provide your script file, or a description of which >>>>>>>>>>>>>>>> button you press in the GUI. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Please also provide information about your system with: >>>>>>>>>>>>>>>> relax -i >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Then I will make a tutorial for you. To be added here: >>>>>>>>>>>>>>>> http://wiki.nmr-relax.com/Category:Tutorials >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> If there is a problem in relax, I will write a systemtest >>>>>>>>>>>>>>>> which will solve the problem. >>>>>>>>>>>>>>>> And the problem will never return. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> If this a user error, the tutorial should help to prevent >>>>>>>>>>>>>>>> this, and would be the first step before >>>>>>>>>>>>>>>> adding/modifying the manual. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Regarding using mpirun. >>>>>>>>>>>>>>>> Have a look at this page. Maybe it helps. >>>>>>>>>>>>>>>> http://wiki.nmr-relax.com/OpenMPI >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Cheers. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> 2016-09-03 4:13 GMT+02:00 Mahdi, Sam < >>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hello everyone, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> So I was able to set up and run the dauvergne_protocol >>>>>>>>>>>>>>>>> successfully by >>>>>>>>>>>>>>>>> using the script in the wiki. The problem I have come >>>>>>>>>>>>>>>>> across now is the >>>>>>>>>>>>>>>>> program doesn't seem to read my data. Using the gui >>>>>>>>>>>>>>>>> interface I was able to >>>>>>>>>>>>>>>>> successfully load my data and run it. When I upload my >>>>>>>>>>>>>>>>> data using the >>>>>>>>>>>>>>>>> script command: >>>>>>>>>>>>>>>>> relax_data.read(ri_id='R1_Agne >>>>>>>>>>>>>>>>> s',ri_type='R1',frq=599.642*1e6, >>>>>>>>>>>>>>>>> file='R1_Agnes',res_num_col=1,data_col=2,error_col=3) >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> The output file simply gives errors for amino acids I >>>>>>>>>>>>>>>>> don't have data for: >>>>>>>>>>>>>>>>> RelaxWarning: The sequence data in the line ['1'] is >>>>>>>>>>>>>>>>> invalid, the data is >>>>>>>>>>>>>>>>> missing. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> This is fine as relax just ignores these values and >>>>>>>>>>>>>>>>> continues its >>>>>>>>>>>>>>>>> calculations. I only receive this warning for values I >>>>>>>>>>>>>>>>> don't have data for. >>>>>>>>>>>>>>>>> This is the same thing I got when using the gui interface >>>>>>>>>>>>>>>>> (the gui however >>>>>>>>>>>>>>>>> showed my values that I have data for and the residue it >>>>>>>>>>>>>>>>> corresponds to, >>>>>>>>>>>>>>>>> using the script I don't receive such an output, I don't >>>>>>>>>>>>>>>>> know whether this >>>>>>>>>>>>>>>>> is normal or not). However, since I don't get this warning >>>>>>>>>>>>>>>>> for every amino >>>>>>>>>>>>>>>>> acid, I assume this means it has read the values for the >>>>>>>>>>>>>>>>> other amino acids. >>>>>>>>>>>>>>>>> All of my data is the same, relax warnings only pop up for >>>>>>>>>>>>>>>>> amino acids that >>>>>>>>>>>>>>>>> I don't have data for. The problem is, when I enter the >>>>>>>>>>>>>>>>> dAuvergne protocol, >>>>>>>>>>>>>>>>> I get the protocol working, it starts running local_tm >>>>>>>>>>>>>>>>> however it appears >>>>>>>>>>>>>>>>> none of my data has been uploaded: >>>>>>>>>>>>>>>>> RelaxWarning: The spin '#hRGS7:2@N' has been deselected >>>>>>>>>>>>>>>>> because of missing >>>>>>>>>>>>>>>>> relaxation data >>>>>>>>>>>>>>>>> RelaxWarning: The spin '#hRGS7:3@N' has been deselected >>>>>>>>>>>>>>>>> because of missing >>>>>>>>>>>>>>>>> relaxation data >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> And I get that warning for every single amino acid. From >>>>>>>>>>>>>>>>> the output, it >>>>>>>>>>>>>>>>> appears to have read the file since it knows exactly which >>>>>>>>>>>>>>>>> amino acids I >>>>>>>>>>>>>>>>> don't have data for, but I don't know why when it comes to >>>>>>>>>>>>>>>>> running the >>>>>>>>>>>>>>>>> protocol, it tells me I havn't inputed any data. I have >>>>>>>>>>>>>>>>> typed everything >>>>>>>>>>>>>>>>> directly according to the script from the wiki. From >>>>>>>>>>>>>>>>> running the protoco, >>>>>>>>>>>>>>>>> it appears everything has properly been uploaded, >>>>>>>>>>>>>>>>> structure data, magnetic >>>>>>>>>>>>>>>>> dipole interactions, csa, the data pipe, the analysis >>>>>>>>>>>>>>>>> variables, the python >>>>>>>>>>>>>>>>> module imports, and setting up the spins from the pdb >>>>>>>>>>>>>>>>> file. It appears the >>>>>>>>>>>>>>>>> only error is from loading the actual relaxation data. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On a completely unrelated side note, I have been >>>>>>>>>>>>>>>>> attempting to run relax on >>>>>>>>>>>>>>>>> multiple processors. I have tried 2 different computers, >>>>>>>>>>>>>>>>> both fedora linux. >>>>>>>>>>>>>>>>> I have mpi4py and openmpi downloaded on both. On one, I >>>>>>>>>>>>>>>>> can get relax on >>>>>>>>>>>>>>>>> multiple cores working (havn't been able to successfully >>>>>>>>>>>>>>>>> run it due to >>>>>>>>>>>>>>>>> being unable to upload any data properly). On the other >>>>>>>>>>>>>>>>> however, I type in >>>>>>>>>>>>>>>>> the mpirun -np --multi='mpi4py' script, but I get no >>>>>>>>>>>>>>>>> output. I can see that >>>>>>>>>>>>>>>>> it's running in the background (top command), but nothing >>>>>>>>>>>>>>>>> pops up, no text >>>>>>>>>>>>>>>>> command, nothing. I typed the same mpirun with the --gui, >>>>>>>>>>>>>>>>> but that opened >>>>>>>>>>>>>>>>> up nothing. On a uni-processor (typing in the exact same >>>>>>>>>>>>>>>>> command without >>>>>>>>>>>>>>>>> indicating how many cores i.e. no -np --multi='mpi4py') it >>>>>>>>>>>>>>>>> works just fine, >>>>>>>>>>>>>>>>> so I don't think its my openmpi that's an issue. I don't >>>>>>>>>>>>>>>>> know whether this >>>>>>>>>>>>>>>>> is an issue with my mpi4py or a personal computer issue >>>>>>>>>>>>>>>>> (since on the other >>>>>>>>>>>>>>>>> computer relax runs just fine on multiple cores). >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Sincerely, >>>>>>>>>>>>>>>>> Sam >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> P.S. when I do enter the top command to see what's >>>>>>>>>>>>>>>>> running. My master shows >>>>>>>>>>>>>>>>> mpirun, and the 3 slaves display python when I put -np 4, >>>>>>>>>>>>>>>>> so I know >>>>>>>>>>>>>>>>> something is running in the background. I have 8 cores. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Wed, Aug 31, 2016 at 6:49 PM, Mahdi, Sam < >>>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu> >>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> > Hello everyone, >>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>> > I am attempting to run relax on a multi-processor mode. >>>>>>>>>>>>>>>>> I have been able >>>>>>>>>>>>>>>>> > to successfully set-up relax to operate in a >>>>>>>>>>>>>>>>> multi-processor mode by using >>>>>>>>>>>>>>>>> > the mpirun -np #ofprocessors /location/of/relax >>>>>>>>>>>>>>>>> --multi='mpi4py' >>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>> > The problem I encounter is when using the --tee log >>>>>>>>>>>>>>>>> dauvergne_protocol.py >>>>>>>>>>>>>>>>> > command. I receive this error >>>>>>>>>>>>>>>>> > RelaxError: the script file 'dauvergne_protocol.py' does >>>>>>>>>>>>>>>>> not exist >>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>> > I located the script file and tried to direct to it's >>>>>>>>>>>>>>>>> path >>>>>>>>>>>>>>>>> > mpirun /usr/local/Relax/relax-2.2.5/relax >>>>>>>>>>>>>>>>> --multi='mpi4py' --tee log >>>>>>>>>>>>>>>>> > /usr/local/Relax/relax-2.2.5/a >>>>>>>>>>>>>>>>> uto-analyses/dauvergne_protocol.py >>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>> > But i received this error >>>>>>>>>>>>>>>>> > RelaxError: the script file >>>>>>>>>>>>>>>>> '/usr/local/Relax/relax-2.2.5/ >>>>>>>>>>>>>>>>> > auto-analyses/dauvergne_protocol.py' does not exist. >>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>> > Even though I have the script, it doesn't seem to be >>>>>>>>>>>>>>>>> able to locate it. >>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>> > On a side note, in the manual, one dash doesn't actually >>>>>>>>>>>>>>>>> run the command. >>>>>>>>>>>>>>>>> > I.e. in the manual it displays -multi='mpi4py' . What it >>>>>>>>>>>>>>>>> should be is >>>>>>>>>>>>>>>>> > --multi='mpi4py' . The same goes for -tee. It should be >>>>>>>>>>>>>>>>> --tee. >>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>> > Sincerely, >>>>>>>>>>>>>>>>> > Sam >>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>> relax (http://www.nmr-relax.com) >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> This is the relax-users mailing list >>>>>>>>>>>>>>>>> relax-users@gna.org >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> To unsubscribe from this list, get a password >>>>>>>>>>>>>>>>> reminder, or change your subscription options, >>>>>>>>>>>>>>>>> visit the list information page at >>>>>>>>>>>>>>>>> https://mail.gna.org/listinfo/relax-users >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>> >>> >> > _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users